How to Process .nc (NetCDF) Files in MATLAB

NetCDF (Network Common Data Form) is a multidimensional binary format used for climate, oceanographic, and geospatial data. MATLAB provides high-level functions (ncdisp, ncinfo, ncread, ncwrite) to inspect, read, slice, and plot this data.

1. Inspect Metadata and Structure

Always inspect the variables, dimensions, and attributes inside the file before loading data into memory.

filename = 'climate_data.nc';

% Print entire schema to the command window
ncdisp(filename);
% Store metadata programmatically in a struct
info = ncinfo(filename);
% List all variable names
varNames = {info.Variables.Name};
disp('Variables found in file:');
disp(varNames');

2. Read Data Variables and Attributes

Extract coordinates and measurement matrices using ncread() and attribute metadata with ncreadatt().

% Read coordinate grids
lon = ncread(filename, 'lon');
lat = ncread(filename, 'lat');
time = ncread(filename, 'time');

% Read main data matrix (e.g., Sea Surface Temperature)
sst = ncread(filename, 'sst');
% Read missing value attribute (_FillValue or missing_value)
fillVal = ncreadatt(filename, 'sst', '_FillValue');
% Replace fill values with NaN for accurate calculation and plotting
sst(sst == fillVal) = NaN;

3. Read a Subset (Hyperslab) for Large Files

When files are too large to fit in memory, specify start and count vectors to extract only the target time step or geographic bounding box.

% Syntax: ncread(filename, varName, start_indices, count_values, [stride])

% Example: Read all lon (360), all lat (180), but only the 1st time step
startIdx = [1, 1, 1];
countIdx = [Inf, Inf, 1]; % Inf reads the full length along that dimension
sst_timestep1 = ncread(filename, 'sst', startIdx, countIdx);

4. Plot 2D Spatial NetCDF Grids

Plot geographic coordinates using imagesc() or contourf().

figure('Color', 'w', 'Position', [100, 100, 750, 420]);

% Transpose matrix to match [lat, lon] grid indexing
imagesc(lon, lat, sst_timestep1');
set(gca, 'YDir', 'normal'); % Correct upside-down latitude orientation
colormap('jet');
cb = colorbar;
ylabel(cb, 'Temperature (K)');
xlabel('Longitude');
ylabel('Latitude');
title('NetCDF Spatial Grid: Sea Surface Temperature');
grid on;

5. Create and Write New NetCDF Files

To export computed results into a standard NetCDF file, define dimensions with nccreate() and write data with ncwrite().

outFile = 'output_results.nc';

% Define dimensions
nccreate(outFile, 'temperature', ...
    'Dimensions', {'lon', 360, 'lat', 180, 'time', 12}, ...
    'Datatype', 'single', ...
    'Format', 'netcdf4_classic');
% Write data into variable
dummyData = single(rand(360, 180, 12));
ncwrite(outFile, 'temperature', dummyData);
% Write metadata attributes
ncwriteatt(outFile, 'temperature', 'units', 'degrees_Celsius');
ncwriteatt(outFile, 'temperature', 'description', 'Simulated monthly mean temperature');

Core NetCDF Functions Summary